software-review coevolve: Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan'

Submitting Author Name: Scott Claessens Submitting Author Github Handle: @ScottClaessens Other Package Authors Github handles: @ErikRingen Repository: https://github.com/ScottClaessens/coevolve Version submitted: 0.1.0.9005 Submission type: Stats Badge grade: gold Editor: @natydasilva Reviewers: TBD Due dates: TBD Archive: TBD Version accepted: TBD Language: en

Package: coevolve
Title: Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan'
Version: 0.1.0.9005
Authors@R: 
    c(person("Scott", "Claessens", , "[email protected]", 
             role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3562-6981")),
      person("Erik", "Ringen", , "[email protected]", 
             role = c("aut")))
Description: Fit Bayesian generalized dynamic phylogenetic models using 'Stan'. 
    The package allows an abritrary number of variables with different response 
    distributions to coevolve on a phylogenetic tree via an Ornstein-Uhlenbeck 
    evolutionary process, allowing users to assess directionality between 
    coevolving variables.
License: GPL (>= 3)
URL: https://github.com/ScottClaessens/coevolve, https://scottclaessens.github.io/coevolve/
BugReports: https://github.com/ScottClaessens/coevolve/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd", "srr::srr_stats_roclet"))
RoxygenNote: 7.3.2
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    tibble,
    withr
Config/testthat/edition: 3
Imports: 
    ape,
    bayesplot,
    cmdstanr,
    colorspace,
    dplyr,
    ggplot2,
    gridExtra,
    Matrix,
    methods,
    patchwork,
    phangorn,
    phaseR,
    phytools,
    posterior,
    purrr,
    readr,
    rlang,
    stats,
    stringr,
    tidyr
VignetteBuilder: knitr
Depends: 
    R (>= 3.5.0)
LazyData: true
Additional_repositories: https://stan-dev.r-universe.dev/
Remotes:
    stan-dev/cmdstanr,
    mjg211/phaseR

Scope

Please indicate which of our statistical package categories this package falls under. (Please check one or more appropriate boxes below):

Statistical Packages
- [x] Bayesian and Monte Carlo Routines
- [ ] Dimensionality Reduction, Clustering, and Unsupervised Learning
- [ ] Machine Learning
- [ ] Regression and Supervised Learning
- [ ] Exploratory Data Analysis (EDA) and Summary Statistics
- [ ] Spatial Analyses
- [ ] Time Series Analyses
- [ ] Probability Distributions

Pre-submission Inquiry

[x] A pre-submission inquiry has been approved in issue #715

General Information

Who is the target audience and what are scientific applications of this package?

The target audience is researchers in the life sciences and cultural evolution who would like to model how multiple variables have coevolved over evolutionary time. The coevolve package allows users to fit Bayesian generalised dynamic phylogenetic models in Stan. These models estimate the autoregressive and cross-lagged effects of variables along the branches of a phylogenetic tree. The current version of the package allows users to model different data types (e.g., binary, ordinal, continuous, count) while accounting for measurement error, missing data, and repeated measures.

Paste your responses to our General Standard G1.1 here, describing whether your software is:

This is the first implementation of a novel algorithm.

(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

I don't think these guidelines apply to this package.

Badging

What grade of badge are you aiming for?

gold

If aiming for silver or gold, describe which of the four aspects listed in the Guide for Authors chapter the package fulfils (at least one aspect for silver; three for gold)

Compliance with a good number of standards beyond those identified as minimally necessary.
Demonstrating excellence in compliance with multiple standards from at least two broad sub-categories.
Internal aspects of package structure and design.

Technical checks

Confirm each of the following by checking the box.

[x] I have read the rOpenSci packaging guide.
[x] I have read the author guide and I expect to maintain this package for at least 2 years or have another maintainer identified.
[x] I/we have read the Statistical Software Peer Review Guide for Authors.
[x] I/we have run autotest checks on the package, and ensured no tests fail.
[x] The srr_stats_pre_submit() function confirms this package may be submitted.
[x] The pkgcheck() function confirms this package may be submitted - alternatively, please explain reasons for any checks which your package is unable to pass.

Currently, the pkgcheck() function is failing due to a failing R CMD check workflow run on macOS. We are hoping that this is temporary failure due to GitHub runner caching.

This package:

[x] does not violate the Terms of Service of any service it interacts with.
[x] has a CRAN and OSI accepted license.
[x] contains a README with instructions for installing the development version.

Publication options

[x] Do you intend for this package to go on CRAN?
[ ] Do you intend for this package to go on Bioconductor?

Code of conduct

[x] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Jul 24 '25 10:07 ScottClaessens

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

Jul 24 '25 10:07 ropensci-review-bot

:rocket:

Editor check started

:wave:

Jul 24 '25 10:07 ropensci-review-bot

Checks for coevolve (v0.1.0.9005)

git hash: 097c50f4

:heavy_check_mark: Package name is available
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_multiplication_x: Package fails continuous integration checks.
:heavy_check_mark: Package coverage is 98.2%.
:heavy_check_mark: This is a statistical package which complies with all applicable standards
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Some goodpractice linters failed.
:eyes: Function names are duplicated in other packages
:eyes: Package has unusually large number of 20 Imports (> 98% of all packages)

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL (>= 3)

1. rOpenSci Statistical Standards (`srr` package)

This package is in the following category:

Bayesian and Monte Carlo

:heavy_check_mark: All applicable standards [v0.2.0] have been documented in this package (470 complied with; 24 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

2. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	329
internal	coevolve	44
internal	utils	28
internal	graphics	6
internal	grDevices	2
imports	ggplot2	46
imports	stats	30
imports	posterior	15
imports	dplyr	7
imports	stringr	7
imports	ape	4
imports	cmdstanr	3
imports	Matrix	2
imports	phangorn	2
imports	tidyr	2
imports	bayesplot	1
imports	purrr	1
imports	readr	1
imports	colorspace	NA
imports	gridExtra	NA
imports	methods	NA
imports	patchwork	NA
imports	phaseR	NA
imports	phytools	NA
imports	rlang	NA
suggests	tibble	2
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	withr	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

for (33), c (26), length (18), names (18), seq_along (16), paste0 (13), list (12), which (12), is.na (11), t (9), ncol (8), nrow (7), seq_len (7), apply (6), as.character (6), as.numeric (6), colnames (6), drop (6), ifelse (6), rep (6), unlist (6), matrix (5), max (5), mean (5), any (4), factor (4), lapply (4), unique (4), data.frame (3), if (3), is.numeric (3), match (3), deparse (2), duplicated (2), is.null (2), levels (2), min (2), sample (2), scale (2), sub (2), substitute (2), sum (2), all (1), array (1), as.data.frame (1), as.list (1), as.matrix (1), ceiling (1), chol (1), col (1), diag (1), dim (1), dimnames (1), do.call (1), expand.grid (1), formals (1), gsub (1), intersect (1), labels (1), mode (1), numeric (1), paste (1), seq (1), solve (1), sort (1), summary (1), switch (1), tempfile (1), tryCatch (1), vector (1)

ggplot2

element_blank (19), aes (7), element_text (5), theme (3), element_rect (2), guide_colourbar (2), unit (2), after_stat (1), element_line (1), facet_wrap (1), geom_line (1), ggplot (1), theme_classic (1)

coevolve

coev_calculate_theta (3), coev_pred_series (3), coev_make_stancode (2), coev_make_standata (2), extract_samples (2), lmod (2), plot_diag (2), choose_plot_type (1), coev_calculate_delta_theta (1), coev_fit (1), coev_plot_delta_theta (1), coev_plot_flowfield (1), coev_plot_pred_series (1), coev_plot_predictive_check (1), coev_plot_selection_gradient (1), coev_plot_trait_values (1), coev_simulate_coevolution (1), extract_samples.coevfit (1), ou (1), ou_sde (1), plot_lower_tri (1), plot_upper_tri (1), plot.coevfit (1), print_format (1), print.coevfit (1), print.coevsummary (1), run_checks (1), run_checks_data (1), run_checks_dist_cov (1), run_checks_dist_mat (1), run_checks_effects_mat (1), run_checks_id (1), run_checks_measurement_error (1), run_checks_plot_trait_values (1), run_checks_pred_series (1)

stats

median (10), quantile (9), sd (3), mad (2), time (2), line (1), nobs (1), sigma (1), var (1)

utils

data (27), modifyList (1)

posterior

as_draws_rvars (8), draws_of (2), ndraws (2), as_draws_matrix (1), rvar_mad (1), rvar_median (1)

dplyr

sym (5), across (1), group_by (1)

stringr

str_starts (4), str_extract (2), fixed (1)

graphics

text (2), title (2), contour (1), points (1)

ape

keep.tip (1), node.depth (1), node.depth.edgelength (1), read.tree (1)

cmdstanr

write_stan_file (2), cmdstan_model (1)

grDevices

palette (2)

Matrix

expm (1), nearPD (1)

phangorn

Ancestors (2)

tibble

tibble (2)

tidyr

expand_grid (1), pivot_longer (1)

bayesplot

pp_check (1)

purrr

map2 (1)

readr

parse_number (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

3. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

code in R (100% in 23 files) and
2 authors
1 vignette
3 internal data files
20 imported packages
21 exported functions (median 75 lines of code)
82 non-exported functions in R (median 37 lines of code)

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used:

loc = "Lines of Code"
fn = "function"
exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	23	83.6
files_vignettes	2	81.9
files_tests	17	93.3
loc_R	3701	91.3
loc_vignettes	703	84.1
loc_tests	5382	97.9	TRUE
num_vignettes	1	58.4
data_size_total	67929	80.3
data_size_median	8815	77.9
n_fns_r	103	75.5
n_fns_r_exported	21	68.4
n_fns_r_not_exported	82	77.8
n_fns_per_file_r	3	47.6
num_params_per_fn	4	51.1
loc_per_fn_r	41	85.4
loc_per_fn_r_exp	75	87.9
loc_per_fn_r_not_exp	37	83.9
rel_whitespace_R	1	23.3
rel_whitespace_vignettes	24	78.3
rel_whitespace_tests	1	49.6
doclines_per_fn_exp	69	78.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	249	89.9

3a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

4. `goodpractice` and other checks

Details of goodpractice checks (click to open)

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following check_fail:

cyclocomp

Test coverage with covr

Package coverage: 98.23

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
write_model_block	63
run_checks_variables	51
coev_make_standata	41
run_checks_plot_trait_values	37
run_checks_pred_series	36
write_gen_quantities_block	34
coev_plot_flowfield	32
coev_plot_predictive_check	32
coev_pred_series	31
coev_plot_selection_gradient	28
coev_simulate_coevolution	28
run_checks_sim	27
coev_plot_trait_values	26
summary.coevfit	26
write_transformed_pars_block	24
coev_plot_delta_theta	22
run_checks	19
write_transformed_data_block	19
coev_calculate_theta	18
coev_make_stancode	18
coev_plot_pred_series	18
print.coevsummary	18
coev_calculate_delta_theta	17

Static code analyses with lintr

lintr found no issues with this package!

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 3 function names are duplicated in other packages:

- extract_samples from adnuts, tidybayes
- stancode from brms
- standata from brms

Package Versions

package	version
pkgstats	0.2.0.64
pkgcheck	0.1.2.207
srr	0.1.4.8

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.

Jul 24 '25 10:07 ropensci-review-bot

Hi @ScottClaessens, sorry for slow start here. We're trying to find an editor to handle this submission. You'll see progress as soon as that's happened.

Jul 30 '25 09:07 mpadge

Sorry for the delay @ScottClaessens , we've had a lot of editors on vacation this month, but people are trickling back in!

Aug 22 '25 13:08 ldecicco-USGS

@ropensci-review-bot assign @natydasilva editor

Aug 22 '25 13:08 ldecicco-USGS

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@ropensci-review-bot help

Aug 22 '25 13:08 ropensci-review-bot

@ropensci-review-bot assign @natydasilva as editor

Aug 22 '25 13:08 ldecicco-USGS

Assigned! @natydasilva is now the editor

Aug 22 '25 13:08 ropensci-review-bot

@ScottClaessens Sorry about delays in getting back to you here, but can you give us an update of the state of the package? The previous lot of checks showed that CI tests were failing. Has that been fixed? If so, please ask the bot here to check package and confirm that we're good to proceed.

Nov 07 '25 10:11 mpadge

@mpadge Thank you for following up! The package hasn't changed since I submitted this issue.

I just re-ran the CI tests. As before, they pass on Windows and Linux but fail on Mac (see here). From the logs, it's something to do with the phaseR package that was removed from CRAN. I added mjg211/phaseR to Remotes to fix this. You previously suggested that the resulting Mac-specific error was likely a temporary GitHub runner caching issue, but this seems unlikely as it's been a few months now and the issue still hasn't resolved. I'm not entirely sure how to fix this!

Happy to work with you to get this resolved quickly.

Nov 07 '25 12:11 ScottClaessens

Ah, the issue was solved by a very small change to my GitHub workflow. So sorry about that @mpadge!

I can confirm that all checks are now passing in the most recent 0.1.0.9007 version.

Nov 07 '25 13:11 ScottClaessens

@ropensci-review-bot check package

Nov 07 '25 13:11 ScottClaessens

Thanks, about to send the query.

Nov 07 '25 13:11 ropensci-review-bot

:rocket:

Editor check started

:wave:

Nov 07 '25 13:11 ropensci-review-bot

Checks for coevolve (v0.1.0.9007)

git hash: 01568f01

:heavy_check_mark: Package name is available
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_check_mark: Package coverage is 98.2%.
:heavy_check_mark: This is a statistical package which complies with all applicable standards
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Some goodpractice linters failed.
:eyes: Function names are duplicated in other packages
:eyes: Package has unusually large number of 20 Imports (> 98% of all packages)
:eyes: Examples should not use \dontrun{} unless really necessary.

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL (>= 3)

1. rOpenSci Statistical Standards (`srr` package)

This package is in the following category:

Bayesian and Monte Carlo

:heavy_check_mark: All applicable standards [v0.2.0] have been documented in this package (470 complied with; 24 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

2. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	329
internal	coevolve	44
internal	utils	28
internal	graphics	6
internal	grDevices	2
imports	ggplot2	46
imports	stats	30
imports	posterior	15
imports	dplyr	7
imports	stringr	7
imports	ape	4
imports	cmdstanr	3
imports	Matrix	2
imports	phangorn	2
imports	tidyr	2
imports	bayesplot	1
imports	purrr	1
imports	readr	1
imports	colorspace	NA
imports	gridExtra	NA
imports	methods	NA
imports	patchwork	NA
imports	phaseR	NA
imports	phytools	NA
imports	rlang	NA
suggests	tibble	2
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	withr	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

for (33), c (26), length (18), names (18), seq_along (16), paste0 (13), list (12), which (12), is.na (11), t (9), ncol (8), nrow (7), seq_len (7), apply (6), as.character (6), as.numeric (6), colnames (6), drop (6), ifelse (6), rep (6), unlist (6), matrix (5), max (5), mean (5), any (4), factor (4), lapply (4), unique (4), data.frame (3), if (3), is.numeric (3), match (3), deparse (2), duplicated (2), is.null (2), levels (2), min (2), sample (2), scale (2), sub (2), substitute (2), sum (2), all (1), array (1), as.data.frame (1), as.list (1), as.matrix (1), ceiling (1), chol (1), col (1), diag (1), dim (1), dimnames (1), do.call (1), expand.grid (1), formals (1), gsub (1), intersect (1), labels (1), mode (1), numeric (1), paste (1), seq (1), solve (1), sort (1), summary (1), switch (1), tempfile (1), tryCatch (1), vector (1)

ggplot2

element_blank (19), aes (7), element_text (5), theme (3), element_rect (2), guide_colourbar (2), unit (2), after_stat (1), element_line (1), facet_wrap (1), geom_line (1), ggplot (1), theme_classic (1)

coevolve

coev_calculate_theta (3), coev_pred_series (3), coev_make_stancode (2), coev_make_standata (2), extract_samples (2), lmod (2), plot_diag (2), choose_plot_type (1), coev_calculate_delta_theta (1), coev_fit (1), coev_plot_delta_theta (1), coev_plot_flowfield (1), coev_plot_pred_series (1), coev_plot_predictive_check (1), coev_plot_selection_gradient (1), coev_plot_trait_values (1), coev_simulate_coevolution (1), extract_samples.coevfit (1), ou (1), ou_sde (1), plot_lower_tri (1), plot_upper_tri (1), plot.coevfit (1), print_format (1), print.coevfit (1), print.coevsummary (1), run_checks (1), run_checks_data (1), run_checks_dist_cov (1), run_checks_dist_mat (1), run_checks_effects_mat (1), run_checks_id (1), run_checks_measurement_error (1), run_checks_plot_trait_values (1), run_checks_pred_series (1)

stats

median (10), quantile (9), sd (3), mad (2), time (2), line (1), nobs (1), sigma (1), var (1)

utils

data (27), modifyList (1)

posterior

as_draws_rvars (8), draws_of (2), ndraws (2), as_draws_matrix (1), rvar_mad (1), rvar_median (1)

dplyr

sym (5), across (1), group_by (1)

stringr

str_starts (4), str_extract (2), fixed (1)

graphics

text (2), title (2), contour (1), points (1)

ape

keep.tip (1), node.depth (1), node.depth.edgelength (1), read.tree (1)

cmdstanr

write_stan_file (2), cmdstan_model (1)

grDevices

palette (2)

Matrix

expm (1), nearPD (1)

phangorn

Ancestors (2)

tibble

tibble (2)

tidyr

expand_grid (1), pivot_longer (1)

bayesplot

pp_check (1)

purrr

map2 (1)

readr

parse_number (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

3. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

code in R (100% in 23 files) and
2 authors
1 vignette
3 internal data files
20 imported packages
21 exported functions (median 75 lines of code)
82 non-exported functions in R (median 37 lines of code)

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used:

loc = "Lines of Code"
fn = "function"
exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	23	83.4
files_vignettes	2	81.7
files_tests	17	93.0
loc_R	3701	91.0
loc_vignettes	703	83.9
loc_tests	5382	97.8	TRUE
num_vignettes	1	58.2
data_size_total	67929	80.3
data_size_median	8815	77.9
n_fns_r	103	75.4
n_fns_r_exported	21	68.2
n_fns_r_not_exported	82	77.6
n_fns_per_file_r	3	47.5
num_params_per_fn	4	51.2
loc_per_fn_r	41	85.5
loc_per_fn_r_exp	75	87.8
loc_per_fn_r_not_exp	37	84.0
rel_whitespace_R	1	23.0
rel_whitespace_vignettes	24	77.9
rel_whitespace_tests	1	49.2
doclines_per_fn_exp	69	78.8
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	249	89.7

3a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

4. `goodpractice` and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
19169203230	lint.yaml	success	01568f	15	2025-11-07
19169337412	pages build and deployment	success	5d7e67	39	2025-11-07
19169203228	pkgdown.yaml	success	01568f	40	2025-11-07
19169203240	R-CMD-check	success	01568f	121	2025-11-07
19169203237	test-coverage.yaml	success	01568f	17	2025-11-07

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following check_fail:

cyclocomp

Test coverage with covr

Package coverage: 98.23

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
write_model_block	63
run_checks_variables	51
coev_make_standata	41
run_checks_plot_trait_values	37
run_checks_pred_series	36
write_gen_quantities_block	34
coev_plot_flowfield	32
coev_plot_predictive_check	32
coev_pred_series	31
coev_plot_selection_gradient	28
coev_simulate_coevolution	28
run_checks_sim	27
coev_plot_trait_values	26
summary.coevfit	26
write_transformed_pars_block	24
coev_plot_delta_theta	22
run_checks	19
write_transformed_data_block	19
coev_calculate_theta	18
coev_make_stancode	18
coev_plot_pred_series	18
print.coevsummary	18
coev_calculate_delta_theta	17

Static code analyses with lintr

lintr found no issues with this package!

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages:

- extract_samples from adnuts, tidybayes, EpiNow2, psborrow

Package Versions

package	version
pkgstats	0.2.0.68
pkgcheck	0.1.2.239
srr	0.1.4.9

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

Nov 07 '25 13:11 ropensci-review-bot

Hello, just checking in about this package review. We have made some small developmental changes to the package (now v0.1.0.9009) and have a few more additions we would like to make (see here). Are we okay to continue working on the package while it is under review?

Dec 04 '25 16:12 ScottClaessens

coevolve: Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan'

Scope

Pre-submission Inquiry

General Information

Badging

Technical checks

Publication options

Code of conduct

Checks for coevolve (v0.1.0.9005)

1. rOpenSci Statistical Standards (srr package)

2. Package Dependencies

3. Statistical Properties

3a. Network visualisation

4. goodpractice and other checks

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

5. Other Checks

Editor-in-Chief Instructions:

Checks for coevolve (v0.1.0.9007)

1. rOpenSci Statistical Standards (srr package)

2. Package Dependencies

3. Statistical Properties

3a. Network visualisation

4. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

5. Other Checks

Editor-in-Chief Instructions:

1. rOpenSci Statistical Standards (`srr` package)

4. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

1. rOpenSci Statistical Standards (`srr` package)

4. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck